Naming the modules; Mailing lists
Georg Fuellen
fuellen@dali.Mathematik.Uni-Bielefeld.DE
Tue, 25 Feb 1997 13:29:02 +0000 (GMT)
Steve wrote, -re- the draft announcement for the beta release,
> > [ The following DRAFT should be reformatted+edited to reflect any new
> > version of Bio::Seq/Bio::UnivAln; the announcement is just a re-shuffling
> > of the homepage. I HOPE I CAN SEND IT NEXT MONDAY at the latest; Chris ??? ]
> > ========DRAFT bioperl@mole Farewell message==========
>
> > Subject: Bioperl Beta Announcement; Mailing list moved !
>
> The content of the message looks good, but its sheer bulk makes it a bit
> overwhelming. I think that better formatting and layout could help. How
> about a table of contents at the top?
A table of contents at the top is a VERY GOOD idea !
> Similar comments apply to the text of the bioperl web page. I would
> suggest making the page 1/10th of its current length, and putting all the
> details onto sub-pages; details below
I'd rather not like to do this; adding a TOC should suffice ?! The main reason
is that updating becomes more messy if there are a lot of pages; and I could
no longer just overwrite one page via netscape whenever you desire an update.
Also, a lot of ppl love longer pages b/c they can print them out in one go.
ok? If no, will change this asap.
> Contents of this Message:
>
> 1. Bio::Seq and Bio::UnivAln in public beta
> 2. Bioperl mailing list moved
> 3. Bio::Seq and Bio::UnivAln bet release announcement
> 4. How to get more information
>
> > Dear subscriber to bioperl@mole.bio.cam.ac.uk,
> >
> > 1) Bio::Seq (Sequences) and Bio::UnivAln (Alignments) are now in beta-status,
> > see the announcement below. If you use the code, please mail us feedback !
> Change to:
>
> 1. The bioperl modules for sequences and alignments (Bio::Set) and
Seq
> (Bio::UnivAln) have now been released for beta testing. They have
> just been uploaded to CPAN sites.
>
> 2. The bioperl mailing list is being reorganized and the old
> bioperl@mole.bio.cam.ac.uk list is going away entirely. Replacing it
> is the list 'vsns-bcd-perl-announce,' a moderated list with
> announcements about bioperl. To be removed from the list, send this
> mail (including headers) to:
> fuellen@dali.mathematik.uni-bielefeld.de.
>
> In addition, the unmoderated list vsns-bcd-perl is for people
> interested in acutally developing bioperl code. You can join that
USING and DEVELOPING ...
I feel that we need a list for user's questions, and there are not enough ppl
yet to mandate a split users<->developers. (Since the interaction users<->
developers is very useful, especially in the early stages, a split should
only be done if too much mail is created.)
If you feel there should be a split, we should have vsns-bcd-perl for users,
and vsns-bcd-perl-guts for the developers.
I agree w/ all the other text.
> list by sending mail to:
> majordomo@lists.uni-bielefeld.de
> with the body text:
> subscribe vsns-bcd-perl
>
>
> 3. Information about Bio::Seq and Bio::UnivAln
>
> > Bio::Seq, a Perl module for reading, parsing,
> > writing, slicing, and manipulating single
> > biosequences.
> > Status: beta code, Version 0.020 from 12
> > Febr 97.
> > Special features: manipulate and parse
> > biological sequences
> > In progress: Tight integration with ReadSeq
> > program, robust formatting and output
> > Chief Developer ("Pumpkin Holder"):
> > Chris Dagdigian, cdagdigian@genetics.com.
> >
> > Bio::UnivAln, a Perl module for reading,
> > parsing, writing, slicing, and manipulating
> > multiple biosequences (sequence bags and
> > alignments).
> > Status: beta code, Version 1.002 from 21
> > Febr 97.
> > Very flexible slicing, mapping, consensus,
> > (in)variable sites, gap-free sites, reverse,
> > complement, and reverse complement.
> > Of special interest: You can specify
> > functions for the slicing operation, e.g. use a
> > function that returns true if column
> > characters are "different" according to
> > some definition of yours, and slice all the
> > other columns off... Voila - you have the
> > variable sites only !
> > Also, you can apply a function to some
> > columns and/or rows, and receive the list of
> > function values. E.g. use a function that
> > returns the majority residue based on your
> > own criteria, apply it to the columns, and
> > there you go: Your consensus sequence !
> > Planned enhancements: More
> > CGI/Graphics stuff (a CGI script is in alpha
> > status); implement an option to use the Perl
> > Data Language for the internal
> > representation -> better performance, but
> > you need C installed.
> > Also planned: ReadSeq for format
> > handling, sequence alphabet checks,
> > internal support for more formats e.g. Nexus.
> > Chief Developer ("Pumpkin Holder"):
> > Georg Fuellen,
> > fuellen@Techfak.Uni-Bielefeld.DE,
> > fuellen@dali.mathematik.uni-bielefeld.de.
> >
>
> ^^^^^^^ format all of this to use more columns. Right now it is too
> long. Also, exdent the first line of each topic -- paragraphs are very
> difficult to identify!
Correct; I'll beautify the final version !
> *** Delete all of the text from here until until my next comment
> > Manipulation of Phylogenetic data, and more
> > graphics/www stuff is in the pipeline.
> >
> > For all modules, you will need Perl 5.002
> > installed.
> >
> >
> > There's a developer's list
> > vsns-bcd-perl@lists.uni-bielefeld.de, to which you
> > can subscribe by sending email to
> > majordomo@lists.uni-bielefeld.de, with no subject
> > line, and the following message body: subscribe
> > vsns-bcd-perl
> > Significant updates will be announced on the list
> > vsns-bcd-perl-announce, to which you can subscribe
> > by sending email to
> > majordomo@lists.uni-bielefeld.de, with no subject
> > line, and the following message body: subscribe
> > vsns-bcd-perl-announce
> >
> > About the project.
> >
> > We develop free software, in particular for handling
> > biosequence and alignment data. Perl is an excellent
> > "Glue Language" for interfacing C/Fortran code,
> > WWW/CGI, graphics (e.g. using PGPERL), numerical
> > analysis (e.g. using the Perl Data Language),
> > Java-based GUIs (just dreaming :-), and much more.
> > With the current development of a true Perl Compiler,
> > it is a serious competitor to C: it's got high-level
> > features, and relieves you from manual memory
> > management, segmentation faults, bus errors, most
> > portability problems, etc, etc. So much for the
> > prospects :-)
> >
> > About us.
> >
> > We are loosely associated with the award-winning
> > VSNS-BCD BioComputing Courses; some students of
> > the 1996 course (Chris Dagdigian, Richard Resnick,
> > Lew Gramer, and others) have contributed code and
> > commentary, and the project is co-coordinated by
> > Georg Fuellen, one of the VSNS-BCD organizers.
> > Steven Brenner acts as the chief coordinator; he's
> > currently on travel but will be back online soon.
> **** Delete through here
ok.
> 4. More information about the bioperl project (including the
> mailing list charter, details about the projects and its
> contributers, and -- of course -- the modules themselves)
> can be obtained from the bioperl hompage:
>
> http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/
>
> Note: Do NOT include the welcome.html
As it happens, all stuff is automatically mirrored in USA and Italy,
as part of the VSNS-BCD mirroring system. However, in USA, index.html
is the default for the welcome page, and since there's no such file,
http://merlin.mbcr.bcm.tmc.edu:8001/bcd/Perl/Bio/ will yield a directory
listing, so I always include the welcome.html to avoid confusion !
Therefore, the Q. is: do you feel an advantage if we ever mention these
mirrors ? If no - let's drop the welcome.html.
> > best wishes,
> > georg
> ^^^^ give your last name here; most people don't know hwo georg is!
heh, the last name appears in the next line..?:) Will rethink my .sig :-)
> > fuellen@dali.Mathematik.Uni-Bielefeld.DE, fuellen@Techfak.Uni-Bielefeld.DE
> ^^^^ there's no reason to give two addresses -- it doesn't help anything.
> Just give one.
It helps; Techfak support has been very quick in deleting accounts in the
past, although I hope I can keep it rather long since I really need it;
OTOH, Techfak should be mentioned b/c I'm formally not in the maths department.
> > http://www.techfak.uni-bielefeld.de/techfak/persons/fuellen/georgF.html
> >
>
>
> -------------
> > ===========Welcome message vsns-bcd-perl-announce============
> > Welcome !
> >
> > For more information, please take a look at
>
> I would include a lot more informaiton here. First, give a brief
> introduction to the bioperl projects (2 sentences). The explain the list
> (2 sentences), and point people towards a charter (similar to the old one
> at http://scop.mrc-lmb.cam.ac.uk/pub/bioperl/)
>
> Then tell people where to go for more informaiton.. the bioperl homepage
> and the archives.
Note that this means double work in updating; no time for that I think !
(Better a short welcome message than an outdated one.)
There should definitely be a pointer to a general mailing list charter
(no spams, etc), if you prepare one.
> > A hypermail archive of this list is available at
> > http://www.hrz.uni-bielefeld.de/mailinglists/BCD/vsns-bcd-perl-announce/index.html
> >
> > best wishes,
> > georg
> > fuellen@dali.mathematik.uni-bielefeld.de fuellen@mit.edu
> > http://www.TechFak.Uni-Bielefeld.DE/techfak/persons/fuellen/georgF.html
> >
>
>
> ---
> > ============Module list entry======================
> > Bio::
> > ::Seq bmpO Handle molecular sequences (DNA,RNA,protein) VSNSBCD
> > ::UnivAln bmpO Handle alignments of molecular sequences VSNSBCD
> >
> > VSNSBCD The Bioperl Project mailing list
> > Mail to majordomo@lists.uni-bielefeld.de with body
> > "subscribe vsns-bcd-perl". There is an announcement-only
> > low-volume mailing list too, mail with body
> > "subscribe vsns-bcd-perl-announce" instead.
>
> Looks good, except, I'm going to change the VSNSBCD to just Bioperl.
Ok, although I'd love to see VSNSBCD mentioned... But life is a compromise :)
> ---
>
> Regarding the homepage. Right now it is long and cluttered -- and I find
> that the color scheme makes things hard to read (but is kind of neat).
I'll add a TOC next. I'll also change the background.
> I would split the page into many sub-pages and make it much more
> user-friendly.
See above.
> There should probably be separate subpages for
>
> 1. Introduction
> 2. Current modules
> 3. Mailing list
> 4. Related sites
> 5. Contributors and sponsor
>
> Right now, I find the text to be much to casual. Well intentioned, but
> difficult to read quickly. I would strip out all the smileys and all of
> the comments which require smilies. In general, there should be fewer
> sentences (which won't be read anyway) and more headers and outline bullet
> points (which help people find what they're looking for).
Your points are well-taken; will strip some sentences, too.
> ---
>
> Please let me know once all of my comments on the snail-mails have been
> considered and either implemented or rejected. Once there are bundled tar
Will try my best keeping track of open issues !
> files, I will test them myself and then upload them to CPAN.
First, we need to resolve the following
>>>>>>>>
[I wrote] [...]
http://world.std.com/~swmcd/steven/Perl/module_mechanics.html
also reflects that resentment, and the offerings -re-
``Building Related Perl Modules'' and
``Testing a module from a Perl program'' made me feel uneasy.
But as the page's author says, ``You get used to it. Really.'' Oh well.
Maybe you've got better recommandations than the ones on that page ?
<<<<<<<<
As I said, I've run into trouble anyway, getting a variety of make problems.
I'll work again through the module_mechanics recommandations of _you_
recommand them. But maybe it's easier if you just do this yourself, because
then you can set things up in exactly the way you like. I can prepare
a Bio::UnivAln tar file _without_ the PGPLOT stuff as soon as you request it.
> Steve
Steve wrote, -re- my comments about his snail-mail
> > Just 4 comments now:
> > *Pls reload Bio::UnivAln, take another look at consensus() !
> Will try to do soon.
>
> > *Also, the Fasta Regexp: I'm still not sure that mine is wrong !
> Yours is ok; just strange. Also, how does all of this code deal with
> DOS-formatted files (i.e., that end in \r\n).
uh, uh... Have you got a solution for this?
Is it just DOS, or WinNT/Win95 as well ?
> > *Re the last page of the snail: I still think it's easy to extract a column
> > as a string, but I guess it's the last time I'm mentioning that..
> It is not easy to exract a column which corresponds to a desired column in
> one of the sequences. I _always_ index off of one of the sequences, not
> the alignment (whose numbering is arbitrary and would change if a longer
> sequence were added).
I hope that this can easily be worked in by adding a record
{'numbering'}[$seq_number], once numbering is resolved for Bio::Seq. (It
would need proper accessors, like {'names'}{'seqs'}[$seq_number]{'id'} and
...{'desc'} do.)
> > *Re Overlap w/ Bio::Seq: Let's have Bio::Utils ? - But not right now...
> That's fine.
ok.
best wishes,
georg